Nucleic Acids Research 2005 33(6):2003-2011; doi:10.1093/nar/gki501
Published online 6 April 2005
© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org
A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA
Yvonne Ihle,
Oliver Ohlenschläger,
Sabine Häfner,
Elke Duchardt1,
Martin Zacharias2,
Simone Seitz3,
Roland Zell3,
Ramadurai Ramachandran and
Matthias Görlach*
Molekulare Biophysik/NMR-Spektroskopie, Institut für Molekulare Biotechnologie e.V. Beutenbergstraße 11, D-07745 Jena, Germany
1Institut für Organische Chemie, Johann-Wolfgang-Goethe-Universität Marie-Curie-Straße 11, D-60439 Frankfurt/M., Germany
2International University Bremen, School of Engineering and Science Campus Ring 1, D-28759 Bremen, Germany
3Institut für Virologie und Antivirale Therapie, Friedrich-Schiller-Universität Winzerlaer Straße 10, D-07745 Jena, Germany
*To whom correspondence should be addressed. Tel: +49 3641 656220; Fax: +49 3641 656225; Email: mago{at}imb-jena.de
Received December 23, 2004. Revised March 7, 2005. Accepted March 21, 2005.
The 5'-terminal cloverleaf (CL)-like RNA structures are essential for the initiation of positive- and negative-strand RNA synthesis of entero- and rhinoviruses. SLD is the cognate RNA ligand of the viral proteinase 3C (3Cpro), which is an indispensable component of the viral replication initiation complex. The structure of an 18mer RNA representing the apical stem and the cGUUAg D-loop of SLD from the first 5'-CL of BEV1 was determined in solution to a root-mean-square deviation (r.m.s.d.) (all heavy atoms) of 0.59 Å (PDB 1Z30). The first (antiG) and last (synA) nucleotide of the D-loop forms a novel ‘pseudo base pair’ without direct hydrogen bonds. The backbone conformation and the base-stacking pattern of the cGUUAg-loop, however, are highly similar to that of the coxsackieviral uCACGg D-loop (PDB 1RFR) and of the stable cUUCGg tetraloop (PDB 1F7Y) but surprisingly dissimilar to the structure of a cGUAAg stable tetraloop (PDB 1MSY), even though the cGUUAg BEV D-loop and the cGUAAg tetraloop differ by 1 nt only. Together with the presented binding data, these findings provide independent experimental evidence for our model [O. Ohlenschläger, J. Wöhnert, E. Bucci, S. Seitz, S. Häfner, R. Ramachandran, R. Zell and M. Görlach (2004) Structure, 12, 237–248] that the proteinase 3Cpro recognizes structure rather than sequence.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
|
|
 
P. Liu, L. Li, S. C. Keane, D. Yang, J. L. Leibowitz, and D. P. Giedroc
Mouse Hepatitis Virus Stem-Loop 2 Adopts a uYNMG(U)a-Like Tetraloop Structure That Is Highly Functionally Tolerant of Base Substitutions
J. Virol.,
December 1, 2009;
83(23):
12084 - 12093.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
C. D. Amero, J. J. Arnold, I. M. Moustafa, C. E. Cameron, and M. P. Foster
Identification of the oriI-Binding Site of Poliovirus 3C Protein by Nuclear Magnetic Resonance Spectroscopy
J. Virol.,
May 1, 2008;
82(9):
4363 - 4370.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Schwalbe, O. Ohlenschlager, A. Marchanka, R. Ramachandran, S. Hafner, T. Heise, and M. Gorlach
Solution structure of stem-loop {alpha} of the hepatitis B virus post-transcriptional regulatory element
Nucleic Acids Res.,
March 1, 2008;
36(5):
1681 - 1689.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
P. Liu, L. Li, J. J. Millership, H. Kang, J. L. Leibowitz, and D. P. Giedroc
A U-turn motif-containing stem-loop in the coronavirus 5' untranslated region plays a functional role in replication
RNA,
May 1, 2007;
13(5):
763 - 780.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. M. Bailey and W. E. Tapprich
Structure of the 5' Nontranslated Region of the Coxsackievirus B3 Genome: Chemical Modification and Comparative Sequence Analysis
J. Virol.,
January 15, 2007;
81(2):
650 - 668.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
W. J.G. Melchers, J. Zoll, M. Tessari, D. V. Bakhmutov, A. P. Gmyl, V. I. Agol, and H. A. Heus
A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA
RNA,
September 1, 2006;
12(9):
1671 - 1682.
[Abstract]
[Full Text]
[PDF]
|
|
|
